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PubMed1997

Computer simulation of neuronal toxicity in the spinal cord.

The use of computers to model biological systems is a relatively new research tool. For example, it is possible to write mathematical systems to model neuronal activity involved in memory and learning and to model blood flow in any organ such as the brain. There is also an interest in designing computer-controlled machines to simulate human activities such as hand movements and vision. One of the most important uses of computer modeling is as a research tool to test hypotheses and aid in formulating new hypotheses. This enables the investigator to apply preliminary tests on several experimental strategies and select for animal experimentation the ones that are most likely to produce unambiguous and interpretable results. In the following article, we describe a computer model of neuron toxicity in the mammalian spinal cord.

Dynorphins↗
PubMed2004

Contact stresses and fatigue life in a knee prosthesis: comparison between in vitro measurements and computational simulations.

The evaluation of contact areas and pressures in total knee prosthesis is a key issue to prevent early failure. The first part of this study is based on the hypothesis that the patterns of contact stresses on the tibial insert of a knee prosthesis at different stages of the gait cycle could be an indicator of the wear performances of a knee prosthesis. Contact stresses were calculated for a mobile bearing knee prosthesis by means of finite element method (FEM). Contact areas and stresses were also measured through in vitro tests using Fuji Prescale film in order to support the FEM findings. The second part of this study addresses the long-term structural integrity of metal tibial components in terms of fatigue life by means of experimental tests and FEM simulations. Fatigue experimental evaluations were performed on Cr-Co alloy tibial tray, based on ISO standards. FEM models were used to calculate the stress patterns. The failure risk was estimated with a standard fatigue criterion on the basis of the results obtained from the FEM calculations. Experimental and computational results showed a positive matching.

Computer Simulation↗
PubMed1990

A computer simulation of the creep process of the cell wall using stress relaxation parameters.

The stress relaxation of the cell wall of pea plants was measured and viscoelastic parameters were obtained according to the stress-relaxation analysis developed by Yamamoto et al. (Plant & Cell Physiol. 1970). The creep process of the cell wall was simulated by a numerical integration using stress-relaxation parameters, because the direct conversion of the stress relaxation process to the creep is impractical. In the conversion, a personal computer was programmed for the Maxwell viscoelastic model with a compiler language. Cell wall creep was measured with a specially constituted apparatus and compared with that calculated by the simulation process. The results suggested that the creep can be reproduced by a computer simulation using the stress-relaxation parameters. Both creep and stress-relaxation properties of plant cell walls can be analyzed by using a single model.

Cell Wall↗
PubMed2003

The predictive utility of computer-simulated exercises for preclinical technique performance.

The objective of this research was to determine if a computerized simulated dental exercise predicts students' subsequent performance in preclinical technique courses. Twenty-nine first-year dental students voluntarily participated in the investigation prior to their first experience with a dental handpiece. These students prepared an ideal Class I amalgam on an ivorine mandibular first molar tooth after viewing ten-minute videotaped instructions. Students completed the Class I amalgam on a computerized dental treatment simulator (SIM). All participants' SIM scores were correlated with sub-test scores of the Dental Admission Test (DAT), predental overall grade point average (GPA), predental Biology/Chemistry/Physics grade point average (BCP), and grades from the first two preclinical laboratory technique courses (Lab 1 and Lab 2). The results showed a significant correlation between the simulator scores and DAT sub-test scores of Academic Average and Total Science, as well as Lab 1 scores. Based on these results, the simulator appears to be a good measure of general cognitive ability, including cognitive ability required to complete uncomplicated preclinical exercises.

Aptitude Tests↗
PubMed2006

Computer simulation of electrical conductivity of colloidal dispersions during aggregation.

The computation approach to the simulation of electrical conductivity of colloidal dispersions during aggregation is considered. We use the two-dimensional diffusion-limited aggregation model with multiple-seed growth. The particles execute a random walk, but lose their mobility after contact with the growing clusters or seeds. The two parameters that control the aggregation are the initial concentration of free particles in the system p and the concentration of seeds psi. The case of psi=1, when all the particles are the immobile seeds, corresponds with the usual random percolation problem. The other limiting case of psi=0, when all the particles walk randomly, corresponds to the dynamical percolation problem. The calculation of electrical conductivity and cluster analysis were done with the help of the algorithms of Frank-Lobb and Hoshen-Kopelman. It is shown that the percolation concentration phi c decreases from 0.5927 at psi=1 to 0 at psi --> 0. Scaling analysis was applied to study exponents of correlation length v and of conductivity t. For all psi>0 this model shows universal behavior of classical 2d random percolation with v approximately t approximately 4/3. The electrical conductivity sigma of the system increases during aggregation reaching up to a maximum at the final stage. The concentration dependence of conductivity sigma(phi) obeys the general effective medium equation with apparent exponent ta(psi) that exceeds t. The kinetics of electrical conductivity changes during the aggregation is discussed. In the range of concentration Pc(phi)<p<0.9527 the time of percolation cluster formation pi c decreases with increasing phi.

Journal Article↗
PubMed2006

Using computational simulation to aid in the prediction of socket fit: a preliminary study.

This study illustrates the use of computational analysis to predict prosthetic socket fit. A simple indentation test is performed by applying force to the residual limb of a trans-tibial amputee through an indenter until the subject perceives the onset of pain. Computational finite element (FE) analysis is then applied to evaluate the magnitude of pressure underlying the indenter that initiates pain (pain threshold pressure), and the pressure at the prosthetic socket-residual limb interface. The assessment of socket fit is examined by studying whether or not the socket-limb interface pressure exceeds the pain threshold pressure of the limb. Based on the computer-aided assessment, a new prosthetic socket is then fabricated and fitted to the amputee subject. Successful socket fit is achieved at the end of this process. The approach of using computational analysis to aid in assessing socket fit allows a more efficient evaluation and re-design of the socket even before the actual fabrication and fitting of the prosthetic socket. However, more thorough investigations are required before this approach can be widely used. A subsequent part of this paper discusses the limitations and suggests future research directions in this area.

Amputation, Surgical↗
PubMedDate not supplied

Designing specific protein kinase inhibitors: insights from computer simulations and comparative sequence/structure analysis.

Protein kinases are important targets for designing therapeutic drugs. We describe here a computational approach to extend the usefulness of a single protein-inhibitor structure in aiding the design of protein kinase inhibitors. This approach is based on using sensitivity analysis to identify the most significant functional groups of a lead compound in accounting for binding affinity and on using comparative sequence/structure analysis to examine whether these functional groups would present specificity. A sensitivity analysis study is similar to genetic or chemical modification experiments in which specific features of a lead compound are modified to examine whether they affect properties such as binding affinity. In this study, the binding affinity was estimated by using an implicit-solvent model in which the electrostatic contributions were obtained by solving the Poisson equation, and the hydrophobic effects were accounted for by using surface-area-dependent terms. The comparative sequence/structure analysis involves the study of the amino acid distributions of a large number of protein kinases (384 in this study) near the ligand-binding sites. This analysis provides useful guiding principles for designing specific inhibitors targeted towards a particular kinase. Here, we illustrate the utility of these computational approaches by applying them to identify the determinants of the recognition between the protein kinase A and two of its inhibitors. One inhibitor, balanol, binds to the ATP-binding pocket. The other, protein kinase inhibitor, binds to the substrate-binding site. These analyses have helped to construct pharmacophore models for mining new drug leads from small-molecule libraries and for suggesting how a lead compound or a peptide inhibitor may be modified to generate selective inhibitors.

Azepines↗
PubMed2005

The interaction of dolomite surfaces with metal impurities: a computer simulation study.

This study investigates the behaviour of selected, morphologically important surfaces of dolomite (CaMg(CO3)2), using computational modelling techniques. Interatomic potential methods have been used to examine impurity substitution at cationic sites in these surfaces. Environmentally prevalent cations were studied to this end, namely Ni2+, Co2+, Zn2+, Fe2+, Mn2+ and Cd2+, all of which are also found as end-member carbonate minerals. Solid-solution substitution was investigated and showed that Cd and Mn will substitute from their end-member carbonate phase at either dolomite cation site. Mn is found to preferentially substitute at Mg sites, in agreement with experimental findings. For Ni2+, Co2+ and Zn2+, the magnitude of substitution energies is approximately equal for all surfaces, with the exception of the (1014) surface. However, for the larger cations, a far greater disparity in substitution energies is observed. At a stepped surface, analogous substitutions were performed and it was found that substitution energies for all impurity cations were reduced, indicating that uptake is more viable during growth. The predominant surface, the (1014), was solvated with a monolayer of water in order to investigate the influence of hydration on substitution energetics. The addition of water changes the relative preference for substitution of the different cations. Under aqueous conditions, the substitution energy is determined by three competing factors, the relative importance of which cannot be predicted without this type of computational investigation.

Calcium Carbonate↗
PubMed2006

[Use of a virtual immersion computer simulator as a model for basic training in laparoscopic urology].

BACKGROUND: to date, it has not been defined the best method for teaching urologic laparoscopy, however it is well recognized that it involves a steep learning curve. METHODS: A course of Laparoscopic Urology was done in our Institute. The program included skill practices in a virtual immersion simulator which evaluated, the score and time to complete each activity. This was done in a group of residents with previous experience with this virtual simulator (group 1) and another group of residents with no experience (group 2). Four different basic tasks were performed in the virtual simulator, which included: coordination, cutting, clip application and performing a simple suture. RESULTS: When we compared the scores between both groups the mean scores for each task were superior in group 1 compared to the group 2, with no statistically significant difference, however when we compared the time to complete each task, it was shorter in group 1 compared to group 2 with a statistically significant difference. CONCLUSIONS: The performance of residents without experience in a virtual simulator was similar to that of previously trained residents, however it takes less time to complete each task as the resident gains experience in these simulators. The use of virtual simulators for laparoscopy training are useful when learning basic techniques allowing the surgeon to improve hand dexterity and coordination in laparoscopic surgery.

Computer Simulation↗
PubMed1990

Computer simulation of Rocky Mountain spotted fever transmission by the American dog tick (Acari: Ixodidae).

A computer model was developed for simulation of the transmission of Rickettsia rickettsii, the causative agent of Rocky Mountain spotted fever (RMSF), by the American dog tick, Dermacentor variabilis (Say). The model of RMSF was combined with a model for population dynamics of the American dog tick and included simulation of infection and transmission of rickettsiae between ticks and host mammals and transmission of RMSF to humans. The model simulated the effects of biotic and environmental variables such as weather, host density, habitat, transovarial transmission, fecundity of infected ticks, and infectivity level of ticks and mammals. Some parameters in the model were fitted by iterative simulations to produce realistic rates of R. rickettsii infection in adult ticks and small and medium-sized mammal hosts. Parameters also were fitted to yield the historical average number of RMSF cases for Virginia. Comparisons of the simulated and actual number of cases for nine other states indicated a reasonable level of validity for the model. A theoretical tick density threshold of 252 unfed adult ticks/ha for transmission of RMSF was determined from a relationship between rate of transmission to humans and density of ticks. The transmission threshold can be used for additional modeling efforts to study the effects of management technologies on tick densities and RMSF human cases. The model can serve as a framework for modeling other tick-borne diseases such as Lyme disease, babesiosis, and heartwater.

Animals↗
PubMed1990

Computer simulation of management strategies for American dog ticks (Acari: Ixodidae) and Rocky Mountain spotted fever.

Computer models were developed to simulate the effects of management technologies on populations of the American dog tick, Dermacentor variabilis (Say), principal vector of Rocky Mountain spotted fever (RMSF) in eastern North America. The technologies modeled were area-wide acaricide application, acaricide-food-baited tubes for self-treatment by small mammals, dipping of dogs in acaricides, acaricide-impregnated plastic dog collars, reduction of small mammal host populations (host management), and removal of vegetation that protects free-living tick stages (vegetative management). Submodels for each of these technologies were incorporated into a model (ADTSIM) for the population dynamics of the tick and RMSF transmission. Comparisons of simulated and observed data were used to verify reasonable accuracy of the submodels. Repetitive simulations were made to identify levels and timing of each control method (alone or combined) required to reduce tick populations below a RMSF transmission threshold of 252 unfed adults/ha. Eight to 30 acaricide applications, depending on acaricide and percentage of population treated, were needed during a 10-yr period to reduce densities of ticks below the threshold. The baited-tube method, host management, and vegetative management (depending on level and frequency of treatment) also were capable of reducing tick density below the threshold. However, acaricide-impregnated plastic dog collars did not reduce tick density below the threshold unless at least 50% of the hosts of adult ticks were domestic dogs. Integrated strategies were developed for management of ticks and RMSF in six selected states. These strategies reduced numbers of human cases of RMSF 90% or more by year 20 by maintaining tick densities between 100 and 252 unfed adults/ha.

Animals↗